Isotropic-nematic phase transition in suspensions of filamentous virus and the neutral polymer Dextran

We present an experimental study of the isotropic-nematic phase transition in an aqueous mixture of charged semi-flexible rods (fd virus) and neutral polymer (Dextran). A complete phase diagram is measured as a function of ionic strength and polymer molecular weight. At high ionic strength we find that adding polymer widens the isotropic-nematic coexistence region with polymers preferentially partitioning into the isotropic phase, while at low ionic strength the added polymer has no effect on the phase transition. The nematic order parameter is determined from birefringence measurements and is found to be independent of polymer concentration (or equivalently the strength of attraction). The experimental results are compared with the existing theoretical predictions for the isotropic-nematic transition in rods with attractive interactions.Comment: 8 Figures. To be published in Phys. Rev. E. For more information see http://www.elsie.brandeis.ed

Spectral phase encoding for data storage and addressing

We propose to use a broad-bandwidth laser source for storing and retrieving multiple holograms in a photorefractive material. Each storage address is defined by a specific spectral encoding of the reference beam. The validity of the spectral encoding method is tested in a preliminary experiment

Prediction of metabolic clusters in early lactation dairy cows using models based on 2 milk biomarkers

The aim of this study was to describe metabolism of early-lactation dairy cows by clustering cows based on glucose, insulin-like growth factor I (IGF-I), free fatty acid, and beta-hydroxybutyrate (BHB) using the k-means method. Predictive models for metabolic clusters were created and validated using 3 sets of milk biomarkers (milk metabolites and enzymes, glycans on the immuno-gamma globulin fraction of milk, and Fourier-transform mid-infrared spectra of milk). Metabolic clusters are used to identify dairy cows with a balanced or imbalanced metabolic profile. Around 14 and 35 d in milk, serum or plasma concentrations of BHB, free fatty acids, glucose, and IGF-I were determined. Cows with a favorable metabolic profile were grouped together in what was referred to as the "balanced" group (n = 43) and were compared with cows in what was referred to as the "other balanced" group (n = 64). Cows with an unfavorable metabolic profile were grouped in what was referred to as the "imbalanced" group (n = 19) and compared with cows in what was referred to as the "other imbalanced" group (n = 88). Glucose and IGF-I were higher in balanced compared with other balanced cows. Free fatty acids and BHB were lower in balanced compared with other balanced cows. Glucose and IGF-I were lower in imbalanced compared with other imbalanced cows. Free fatty acids arid BHB were higher in imbalanced cows. Metabolic clusters were related to production parameters. There was a trend for a higher daily increase in fat- and protein-corrected milk yield in balanced cows, whereas that of imbalanced cows was higher. Dry matter intake and the daily increase in dry matter intake were higher in balanced cows and lower in imbalanced cows. Energy balance was continuously higher in balanced cows and lower in imbalanced cows. Weekly or twice-weekly milk samples were taken and milk metabolites and enzymes (milk glucose, glucose-6-phosphate, BHB, lactate dehydrogenase, N-acetyl-beta-D-glucosaminidase, isocitrate), immunogamma globulin glycans (19 peaks), and Fourier-transform mid-infrared spectra (1,060 wavelengths reduced to 15 principal components) were determined. Milk biomarkers with or without additional cow information (days in milk, parity, milk yield featurs) were used to create predictive models for the metabolic clusters. Accuracy for prediction of balanced (80%) and imbalanced (88%) cows was highest using milk metabolites and enzymes combined with days in milk and parity. The results and models of the present study are part of the GplusE project and identify novel milk-based phenotypes that may be used as predictors for metabolic and performance traits in early-lactation dairy cows

Prediction of key milk biomarkers in dairy cows through milk MIR spectra and international collaborations.

peer reviewedAt the individual cow level, sub-optimum fertility, mastitis, negative energy balance and ketosis are major issues in dairy farming. These problems are widespread on dairy farms and have an important economic impact. The objectives of this study were: 1) to assess the potential of milk Mid Infrared (MIR) spectra to predict key biomarkers of energy deficit (citrate, isocitrate, glucose-6P, free glucose), ketosis (BHB and acetone), mastitis (NAGase and LDH), and fertility (progesterone); 2) to test alternative methodologies to partial least square regression (PLS) to better account for the specific asymmetric distribution of the biomarkers; and 3) to create robust models by merging large data sets from 5 international or national projects. Benefiting from this international collaboration, the data set comprised a total of 9,143 milk samples from 3,758 cows located in 589 herds across 10 countries and represented 7 breeds. The samples were analyzed by reference chemistry for biomarker contents while the MIR analyses were performed on 30 instruments from different models and brands, with spectra harmonized into a common format. Four quantitative methodologies were evaluated to address the strongly skewed distribution of some biomarkers. PLS was used as the reference basis, and compared with a random modification of distribution associated with PLS (Random-downsampling-PLS), an optimized modification of distribution associated with PLS (KennardStone-downsampling-PLS) and Support Vector Machine (SVM). When the ability of MIR to predict biomarkers was too low for quantification, different qualitative methodologies were tested to discriminate low vs high values of biomarkers. For each biomarker, 20% of the herds were randomly removed within all countries to be used as the validation data set. The remaining 80% of herds were used as the calibration data set. In calibration, the 3 alternative methodologies outperform the PLS performances for the majority of biomarkers. However, in the external herd validation, PLS provided the best results for isocitrate, glucose-6P, free glucose and LDH (R2v = 0.48, 0.58, 0.28, and 0.24). For other molecules, PLS-Random-downsampling and PLS-KennardStone-downsampling outperformed PLS in the majority of cases, but the best results were provided by SVM for citrate, BHB, acetone, NAGase and progesterone (R2v = 0.94, 0.58, 0.76, 0.68, and 0.15). Hence, PLS and SVM based on the entire data set provided the best results for normal and skewed distributions, respectively. Complementary to the quantitative methods, the qualitative discriminant models enabled the discrimination of high and low values for BHB, acetone, and NAGase with a global accuracy around 90%, and glucose-6P with an accuracy of 83%. In conclusion, MIR spectra of milk can enable quantitative screening of citrate as a biomarker of energy deficit and discrimination of low and high values of BHB, acetone, and NAGase, as biomarkers of ketosis and mastitis. Finally, progesterone could not be predicted with sufficient accuracy from milk MIR spectra to be further considered. Consequently, MIR spectrometry can bring valuable information regarding the occurrence of energy deficit, ketosis and mastitis in dairy cows, which in turn have major influences on their fertility and survival

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs

Genetic parameters for milk urea and its relationship with milk yield and compositions in Holstein dairy cows

peer reviewe

Time-encoded spatial routing in a photorefractive crystal

The spatial routing of a temporally encoded stream of optical pulses is experimentally demonstrated. The holograms that link the temporally shaped addresses to the def lection directions are engraved in a photorefractive crystal. © 1996 Optical Society of America After the holography concept was clearly extended from the space to the time domain, 1 it appeared difficult to cope experimentally with the fast f low of short signals that represents the restored image of a temporal hologram. For instance, when such a hologram is engraved in a persistent spectral-holeburning material embedded in an amorphous material, the retrieved temporal recording can include .1000 subpicosecond pulses, which are sequentially emitted at a rate greater than 1 Tbit͞s. Fast optical gating techniques were necessary for sampling the temporal structure of the signal f low, 2,3 but they were not appropriate for simultaneously analyzing a spatial image. Only recently was a fast stream of two-dimensional spatial images successfully stored and retrieved within the frame of space and time holography. Recently 9 a scheme was proposed ''to direct temporally structured optical signals originally propagating along a common direction into different and distinct output directions according to the precise temporal waveform encoded onto each signal.'' A detailed explanation of the process, making use of holograms engraved in frequency-selective materials, is given in Ref. 9. However, it has been suggested that the same routing process could be implemented in materials that possess no intrinsic frequency selectivity. Here we use a nonfrequency-selective photorefractive crystal to demonstrate experimentally the routing of data in temporally encoded spatial directions. Also, we show that, despite the subpicosecond scale of the address code, long-duration pulses can be processed in such a material, if their coherence time is short enough to match the time-scale requirements of the router. The storage of a temporal structure in a threedimensional holographic material relies on time -space conversion whereK k 2 2k 1 . The interference pattern is engraved in the crystal as a space-dependent variation of the refractive index, which leads to a Bragg grating of vector 2pnK͞v. In the counterpropagating conf iguration, the grating period is close to l͞2. Let E 2d ͑t͒ be a brief pulse that peaks at t 0. The time integral expresses the sampling analysis of the temporal shape E 1a ͑t͒ through the gate E 2d . The gate location, t K ? r͞v, is scanned as a function of the spatial position along directionK; i.e., the temporal shape E 1a ͑t͒ is recorded as the spatial envelope E 1a ͑K ? r͞v͒ of the Bragg grating. An entire address pulse of duration T can be recorded if its spatial extent vT ͞2 is smaller than the length of the engraved interference pattern. In an exact collinear configuration, the sample thickness L limits the address duration to 2L͞v. Storage is still possible when the waves depart from collinear propagation. Then the condition v͓p 2 ͑k 1 ,k 2 ͔͒T , 2d expresses the trade-off among the maximum object duration T , the collinear propagation angular defect p 2 ͑k 1 ,k 2 ͒, and the beam diameter d. After the programming, the crystal is illuminated by a plane-wave input beam of unit wave vectork 3 k 1